If I remember correctly Emily's Garden is basically a DWC system. I had the same questions when I first started with a DWC system, do you want the starter cube touching the water or not?
I found that for a young seedling with small roots its best to be sure the cube is about 1cm above the water line. Especially if the water is getting fizzy from aeration. It's healthy to get the roots to work to get at the
nutrients. Sometime you have to water the cubes til they get going. If the cube is submerged in the water the new roots won't get any O2.